[2014-04-27 21:53:33] Beginning TopHat run (v2.0.8b)
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[2014-04-27 21:53:33] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 21:53:33] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 21:53:33] Checking for Bowtie index files
[2014-04-27 21:53:33] Checking for reference FASTA file
[2014-04-27 21:53:33] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 21:53:38] Preparing reads
	 left reads: min. length=60, max. length=101, 21889176 kept reads (13774 discarded)
[2014-04-27 22:02:12] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 22:30:26] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 22:34:11] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 22:37:53] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 22:41:28] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 22:45:25] Searching for junctions via segment mapping
[2014-04-27 23:44:37] Retrieving sequences for splices
[2014-04-27 23:46:36] Indexing splices
[2014-04-27 23:47:19] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 23:54:58] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 00:01:48] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 00:08:17] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 00:16:04] Joining segment hits
[2014-04-28 00:24:41] Reporting output tracks
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[2014-04-28 00:37:21] Run complete: 02:43:48 elapsed